4XSZ

Crystal structure of CBR 9393 bound to Escherichia coli RNA polymerase holoenzyme


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.683 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

CBR antimicrobials inhibit RNA polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition.

Bae, B.Nayak, D.Ray, A.Mustaev, A.Landick, R.Darst, S.A.

(2015) Proc.Natl.Acad.Sci.USA 112: E4178-E4187

  • DOI: 10.1073/pnas.1502368112
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center ...

    RNA polymerase inhibitors like the CBR class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. Catalysis by RNA polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound NTP and two Mg(2+) ions from a preinsertion state to a reactive configuration. CBR inhibitors target a crevice between the N-terminal portion of the bridge helix and a surrounding cap region within which the bridge helix is thought to rearrange during the nucleotide addition cycle. We report crystal structures of CBR inhibitor/Escherichia coli RNA polymerase complexes as well as biochemical tests that establish two distinct effects of the inhibitors on the RNA polymerase catalytic site. One effect involves inhibition of trigger-loop folding via the F loop in the cap, which affects both nucleotide addition and hydrolysis of 3'-terminal dinucleotides in certain backtracked complexes. The second effect is trigger-loop independent, affects only nucleotide addition and pyrophosphorolysis, and may involve inhibition of bridge-helix movements that facilitate reactive triphosphate alignment.


    Organizational Affiliation

    The Rockefeller University, New York, NY 10065;,Public Health Research Institute and Department of Microbiology and Molecular Genetics, New Jersey Medical School, Rutgers Biomedical and Health Sciences, Newark, NJ 07103;,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706;,Department of Biochemistry, University of Wisconsin-Madison, Madison, WI 53706; Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706.,The Rockefeller University, New York, NY 10065; darst@rockefeller.edu.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit alpha
A, B, G, H
239Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoA
EC: 2.7.7.6
Find proteins for A7ZSI4 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZSI4
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta
C, I
1342Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoB
EC: 2.7.7.6
Find proteins for A7ZUK1 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZUK1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit beta'
D, J
1407Escherichia coli O139:H28 (strain E24377A / ETEC)Mutation(s): 0 
Gene Names: rpoC
EC: 2.7.7.6
Find proteins for A7ZUK2 (Escherichia coli O139:H28 (strain E24377A / ETEC))
Go to UniProtKB:  A7ZUK2
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
DNA-directed RNA polymerase subunit omega
E, K
91Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks)Mutation(s): 0 
Gene Names: rpoZ
EC: 2.7.7.6
Find proteins for B1IYV1 (Escherichia coli (strain ATCC 8739 / DSM 1576 / Crooks))
Go to UniProtKB:  B1IYV1
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
RNA polymerase sigma factor RpoD
F, L
522Escherichia coli (strain K12)Mutation(s): 0 
Gene Names: rpoD (alt)
Find proteins for P00579 (Escherichia coli (strain K12))
Go to UniProtKB:  P00579
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
42U
Query on 42U

Download SDF File 
Download CCD File 
C, I
4-[3-(4-fluorophenyl)-1H-pyrazol-4-yl]-N-[2-(piperazin-1-yl)ethyl]-2-(trifluoromethyl)aniline
CBR-9393
C22 H23 F4 N5
OXSJLZKYOPQBJE-UHFFFAOYSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
D, J
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
D, J
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.683 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 184.444α = 90.00
b = 206.331β = 90.00
c = 309.607γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

  • Deposited Date: 2015-01-22 
  • Released Date: 2015-07-22 
  • Deposition Author(s): Bae, B., Darst, S.A.

Revision History 

  • Version 1.0: 2015-07-22
    Type: Initial release
  • Version 1.1: 2015-08-05
    Type: Database references
  • Version 1.2: 2015-08-19
    Type: Database references
  • Version 1.3: 2017-11-22
    Type: Derived calculations, Refinement description